1. Introduction to genetic pedigree charts

A pedigree chart is a graphical visualization of a number of people and their genetic relationships. As opposed to social pedigrees, which may include marriages, divorces, children from unmarried relationships, adopted children as well as people who have no children, the focus of genetic pedigrees is on the relevant biological connections between people.

As such, there is only one type of relevant connection between people, namely the connection between a person and their biological parents.

Pedigree Chart Designer by CeGaT GmbH was designed for the creation of such genetic pedigree charts and allows you to model the biological connections between people based on two relationships: parent-parent relationships and parent-child relationships. In addition, each person can be annotated with their disease status and various other details of interest.

2. Creating a pedigree

Start by filling in some basic information about the pedigree, such as the family name (this might save some typing later on when naming individual people), a case number, and a comment describing, e.g., the type of disease afflicting the family. Then draw the pedigree by performing three basic steps covered in more detail below:

Add people to the pedigree

Define relationships between people out of which children are born

Assign children to relationships or single parents.

2.1. Adding people to the pedigree

To add a new person to the pedigree, drag one of the symbols from PCD’s toolbar to the drawing canvas. While dragging, note that a green rectangle indicates where the person will end up when the mouse key is released, while a red rectangle indicates that the person can not be placed at the current mouse location (e.g., because another person is already at that position). Once you place the person on the canvas, the personal details window appears (see 2.2.).

Shortcut: Press CTRL-A to insert a new person at the current mouse position.

2.2. Configuring a person’s details

To configure a person, simply click on the person’s symbol. The personal details window appears. You can edit the person’s name, add a birth date, write one or more lines of comment, define the person’s sex, health status, whether the person is unborn, living, or deceased, as well as indicate whether the person is the index patient.

Shortcut: Place the mouse cursor over a person and press CTRL-G, to change the person’s gender.

Shortcut: Place the mouse cursor over a person and press CTRL-D, to change the person’s status between living and deceased.

Please note that persons are automatically assigned a pedigree identifier of the form X.Y where X is a roman numeral representing the person’s generation and Y is an arabic numeral indicating the position within that generation.

2.3. Defining relationships

To define a relationship between two people, click on one of them. The personal details window appears. Click on „Select partner“, then click on the partner’s name (or pedigree identifier). You can choose whether the two people are consanguine partners.

Shortcut: Place the mouse cursor over a person and press CTRL-R, then click on another person to define a new relationship between the two. Press SHIFT-CTRL-R to define a new consanguinous relationship.

If two people of the same sex are combined in a relationship, the connecting line is drawn in red.

Note that one person can be involved in several relationships.

To remove a relationship, click on one of the partners involved, click on „Remove partner“ and select the relationship you want to remove. Note that this also removes the assignment of all children born from this relationship.

2.4. Assigning children

To create a child-parent-relationship, children can be assigned in different ways, described below:

2.4.1. Assigning a child to a parent relationship

Most commonly, you will want to assign a child to a parent relationship, i.e., identify the child as born from the relationship of a father and a mother. To do this, make sure that the parents’ relationship is defined (see 2.3.). Then click on the child, select on „Make child of“, and select the parents’ relationship from the menu.

Shortcut: Place the mouse cursor over a person and press CTRL-P, then click on the first parent, then on the second parent.

2.4.2. Assigning a child to a single parent

If no information is available on one of the child’s parents, or if only one parent shall be included in the pedigree, a parent relationship may not be available. Instead, you will want to assign a child to a single parent (mother or father) directly. To do this, click on the child, select „Make child of“. Below the defined parent relationships, you will find one entry for each person in the pedigree labelled with that person’s name and an „unknown“ partner. Select one of these.

Shortcut: Place the mouse cursor over a person and press CTRL-P, then click on the single parent, then click again on the single parent.

2.4.3. Defining a child to be a twin of another person

Twins are a special case with specific importance for genetic studies. To define a pair of twins, start by assigning one of the two children to a parent relationship or a single parent as described in 2.4.1 and 2.4.2, respectively.

Then click on the second child, and select „Make twin of“. A menu appears listing all other children in the pedigree. Select the twin and select the type of twin relationship. Twins can be dizygous (normal twins), monozygous (identical twins), or the genetic relationship between the twins may be unknown.

Note that monozygous twins with different sex are connected by a red line.

2.4.4. Removing a child assignment

To remove a child assignment, click on the child’s symbol. Then either assign the child to another parent (see 2.4.1 to 2.4.3.), or click on „Make child of“ and then select „nobody“.

2.4.5. Splitting a pair of twins

To split a pair of twins, you can either assign one of the twins to another parent (see 2.4.1-2.4.3), remove the assignment of one of the twins (see 2.4.4.), or click on the person’s symbol and select „Make twin of“ from the menu, followed by selecting „nobody“.

2.5. Removing a person

To remove a person from the pedigree, click on the person’s symbol and select „Remove this person“ from the menu. Note that this removes all relationships to partners of this person as well as all child assignments to these relationships as well as child assignments involving the removed person as a single parent.

3. Loading, Saving, Printing

3.1. Saving your pedigree to a file

You can save the pedigree by clicking on „Pedigree“-“Save“ or „Save as“.

PCD stores your pedigree in PNG format. PNG graphics files can be imported in many applications (e.g., PowerPoint), edited in graphics applications (e.g., Photoshop), or included in web pages. This allows the pedigree to be viewed by users who are not using PCD.

PCD also stores additional information in the graphics file which allows it to later re-create the contained pedigree chart for further editing (see Technical Details)

3.2. Loading a pedigree from an existing file

You can load a pedigree by clicking on „Pedigree“-“Load“.

Please note that only files created by PCD can be loaded, even though other PNG image files may be visible in the file selection dialog. Furthermore, PCD files that were altered with another application (e.g., Photoshop) will most likely not work since the other application will have removed PCDs additional data fields from the file.

3.3. Printing the pedigree

You can print a pedigree by clicking on „Pedigree“-“Print“. The pedigree will automatically be scaled to fit to the currently selected paper size and orientation (portrait/landscape).

4. Undo/Redo functionality

The „Edit“ menu allows you to undo all changes made since the pedigree was loaded (or created from scratch). It also displays a description of the last modification.

To undo the last modification, open the „Edit“ menu and click on “Undo“.

If you have undone too many modifications, you can redo them (effectively undoing the undo) by opening the „Edit“ menu and clicking on „Redo“.

Shortcut: Press CTRL-Z to undo the latest change.

Shortcut: Press CTRL-Y to redo the undo operation.

5. Biological inconsistensies

PCD draws your attention to biological inconsistensies by rendering parts of the pedigree in red color. These inconsistensies include

Two parents of the same sex

Monozygous twins with different sex

Children which are placed in the same generation as their parents, or a preceding generation.

6. Modifying the pedigree display

6.1. Changing the rendering style

PCD has three different rendering styles. To have your pedigree drawn in a different style, select one of the alternatives from the „View“ menu:

CeGaT style: Relationships are rendered beneath the parents. Personal information is displayed to the right of the person’s pictogram

6.2. Adding a legend

You can add a legend explaining the pedigree pictograms via the „View“ menu. To modify the legend, click on any of its pictograms to edit the description, e.g., to replace „affected“ with the actual name of the disease.

7. Working with multiple phenotypes

PCD can create pedigrees with up to eight independent phenotypes (e.g., epilepsia and deafness). These will be displayed by dividing the person pictograms into equal-sized parts, each displaying the person’s status with respect to one of the phenotypes.

Note that there is a difference in phenotype status between single-phenotype and multi-phenotype pedigrees: Persons in single-phenotype pedigrees can be classified as on of „healthy“, „affected“, „known carrier“, or „unkown“. Persons in multi-phenotype pedigrees can, with respect to each phenotype, be classified as „healthy“, „affected“, „mildly affected“, or „unkown“.

To create a multi-phenotype pedigree, open the „Pedigree“ menu and select „New“. Enter the number of phenotypes for the new pedigree and click ok.

Note that the number of phenotypes can not be changed after persons have been added to the pedigree.

It is advisable to use a legend when working with multi-phenotype pedigrees (see section 6.2.).

8. Technical Details

PCD stores pedigrees in PNG (Portable Network Graphics) format. This allows the pedigrees to be viewed as images in many applications as well as web browsers, and also enables users to further edit their pedigrees using graphics applications (e.g., Photoshop), and to include them in presentations (e.g., using PowerPoint).

In addition, PCD stores a textual representation of the pedigree as meta data in the PNG file in „tEXt“ chunks (for details on the PNG format specification, see [1]). This allows us to later restore the pedigree objects (persons, relationships) from the image file.

However, graphics editing applications usually do not preserve the tEXt chunks. Thus, pedigree PNG files edited with a third party application will most likely not be readable by PCD.

Please note that this means that in addition to the graphical representation of the pedigree in the PNG image, the file also contains a machine-readable representation of the pedigree. This should be considered when sending pedigree files via unsecure networks. As patient confidentiality may be violated, we strongly advise against transmitting pedigree files via unsecure network connections.

9. Java Webstart

PCD is written in the Java language and requires a working Java installation to run. We distribute PCD as Java Webstart application. This is convenient for users as they are always working with the most up-to-date version of the program without having to manually install updates. When starting PCD for the first time, you will be asked whether you trust the issuer of the software. Make sure that you are running the program from the CeGaT GmbH website (https://www.cegat.de) before allowing the program to run.

Pedigree Chart Designer

Dated Aug 31, 2012

This Software License Agreement is a legal agreement (“Agreement”) between you (“You” or “Licensee”, either an individual or a single entity), and CeGaT GmbH, Paul-Ehrlich-Str. 23, 72076 Tübingen (“Licensor” or “CeGaT”). By downloading, installing, or using the PCD Pedigree Chart Designer (together with its accompanying documentation, collectively “PCD” or “Software”), you indicate that you read and accept the provisions of this Agreement and that you agree to be bound by all terms and conditions set forth herein.

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